In April 1940, the Jewish administration took over the pharmacies operating in the ghetto. Apart from Kasperkiewicz's pharmacy at 56 Zgierska Street (which was most likely not reopened due to having been robbed), all of them were incorporated into the Health Department. They were directly subordinate to the Pharmacy Department, headed by Dawid Perelmutter and, from July 1944, by Samuel Kon.

By the end of 1940, there were five pharmacies (Nos. I–V) and one pharmacy warehouse, located in hospital building No. I at 34/36 Łagiewnicka Street, operating in the ghetto. In February 1941, an additional pharmacy, No. VI, was opened. There was also one private pharmacy owned by Samuel Kon and A. Fajneman at 8 Kościelny Square. It was obliged to provide approximately 350 free medicines per day and pay industrial tax to the Finance and Economic Department. Together with the one located in the hospital at 34/36 Łagiewnicka Street, it was one of the largest pharmacies in the ghetto. In the autumn of 1941, it was incorporated into the Department as pharmacy No. VII. Most likely, after the liquidation of the summer camps for children in Marysin, pharmacy No. V was closed down. The pharmacies were open from 8:00 a.m. to 8:00 p.m. They were located at the following addresses:

I – at 9 Stary Rynek (manager: Ita Jedwabowa, MA),
II – at 37 Limanowskiego Street (manager: Aleksander Ostrowski, MA),
III – at 56 Brzezińska Street (manager: Dawid Perelmuter, M.Sc.),
IV – at 36 Łagiewnicka Street (manager: Jakob Kahane, M.Sc.),
V – at 12 Brudzińskiego Street,
VI – at 5 Rybna Street (manager: Natan Otto Blausztejn, M.Sc.),
VII – at 8 Kościelny Square (manager: Samuel Kon, MSc).

In December 1940, the pharmacies employed 76 people: 12 pharmacists, 31 technicians, 1 laboratory assistant, 2 drugstore assistants, 1 accountant, 8 cashiers, 1 labeller and 20 manual workers. Pharmacists were part of a privileged group of the population who received so-called bajrackie (vide Bajrat) allowances. In 1941, pharmacies prepared 633,000 medicines, including nearly 533,000 free of charge. However, this number was still insufficient to meet the needs of the population, and the shortage was particularly acute during epidemics of dysentery, tuberculosis and typhus. Pharmacies struggled with insufficient supplies of medicines. For this reason, medicines were among the most frequently sold goods on the black market.

For a certain period, there was also a pharmacy run by the Special Unit (vide). Its activities were related to the Special Unit's supervision of the distribution of medicines in the ghetto from the beginning of 1943. It was closed down in the first half of August 1943 following a visit by Hans Biebow (vide), who described it as a ‘superfluous institution’.